Mercurial > repos > bgruening > deeptools_plot_pca

comparison plotPCA.xml @ 21:93ce2662f917 draft

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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a
author bgruening
date Wed, 22 Aug 2018 17:00:56 -0400
parents d9376d223fad
children c899e0ccff8c
comparison
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20:aca788d8e71d 21:93ce2662f917
1 <tool id="deeptools_plot_pca" name="plotPCA" version="@WRAPPER_VERSION@.0"> 1 <tool id="deeptools_plot_pca" name="plotPCA" version="@WRAPPER_VERSION@.0" profile="18.01">
2 <description>Generate principal component analysis (PCA) plots from multiBamSummary or multiBigwigSummary output</description> 2 <description>Generate principal component analysis (PCA) plots from multiBamSummary or multiBigwigSummary output</description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">plotPCA</token> 4 <token name="@BINARY@">plotPCA</token>
5 <import>deepTools_macros.xml</import> 5 <import>deepTools_macros.xml</import>
6 </macros> 6 </macros>
20 $advancedOpt.transpose 20 $advancedOpt.transpose
21 $advancedOpt.rowCenter 21 $advancedOpt.rowCenter
22 #if $advancedOpt.colors: 22 #if $advancedOpt.colors:
23 --colors $advancedOpt.colors 23 --colors $advancedOpt.colors
24 #end if 24 #end if
25 #if $advancedOpt.markers:
26 --markers $advancedOpt.markers
27 #end if
25 #end if 28 #end if
26 #if $outFileNameData 29 #if $outFileNameData
27 --outFileNameData '$output_outFileNameData' 30 --outFileNameData '$output_outFileNameData'
28 #end if 31 #end if
29 ]]> 32 ]]>
38 <option value="no" selected="true">no</option> 41 <option value="no" selected="true">no</option>
39 <option value="yes">yes</option> 42 <option value="yes">yes</option>
40 </param> 43 </param>
41 <when value="no" /> 44 <when value="no" />
42 <when value="yes"> 45 <when value="yes">
43 <expand macro="plotWidthHeight" PLOTWIDTH="5.0" PLOTHEIGHT="10.0" /> 46 <expand macro="plotWidthHeight" PLOTWIDTH="10.0" PLOTHEIGHT="10.0" />
44 <param name="PCs" argument="--PCs" label="Principal components to plot" value="1 2" type="text" 47 <param name="PCs" argument="--PCs" label="Principal components to plot" value="1 2" type="text"
45 help="The principal components to plot. If specified, you must provide two different integers, greater than zero, separated by a space. An example (and the default) is '1 2'." /> 48 help="The principal components to plot. If specified, you must provide two different integers, greater than zero, separated by a space. An example (and the default) is '1 2'." />
46 <param name="ntop" argument="--ntop" label="Number of rows to use" value="1000" type="integer" 49 <param name="ntop" argument="--ntop" label="Number of rows to use" value="1000" type="integer"
47 help="Use only the top N most variable rows in the original matrix. Specifying 0 will result in all rows being used. If the matrix is to be transposed, rows with 0 variance are always excluded, even if a values of 0 is specified. The default is 1000." /> 50 help="Use only the top N most variable rows in the original matrix. Specifying 0 will result in all rows being used. If the matrix is to be transposed, rows with 0 variance are always excluded, even if a values of 0 is specified. The default is 1000." />
48 <param name="log2" argument="--log2" type="boolean" truevalue="--log2" falsevalue="" label="log2 transform data" help="log2 transform the datapoints prior to computing the PCA. Note that 0.01 is added to all values to prevent 0 values from becoming -infinity. Using this option with input that contains negative values will result in an error." /> 51 <param name="log2" argument="--log2" type="boolean" truevalue="--log2" falsevalue="" label="log2 transform data" help="log2 transform the datapoints prior to computing the PCA. Note that 0.01 is added to all values to prevent 0 values from becoming -infinity. Using this option with input that contains negative values will result in an error." />
49 <param argument="--transpose" type="boolean" label="Transpose Matrix?" help="Perform the PCA on the transpose of the matrix, (i.e., with samples as rows and features/genes as columns). This then matches what is typically done in R for RNAseq data." truevalue="--transpose" falsevalue="" /> 52 <param argument="--transpose" type="boolean" label="Transpose Matrix?" help="Perform the PCA on the transpose of the matrix, (i.e., with samples as rows and features/genes as columns). This then matches what is typically done in R for RNAseq data." truevalue="--transpose" falsevalue="" />
50 <param argument="--rowCenter" type="boolean" label="Center Rows?" help="When specified, each row (bin, gene, etc.) in the matrix is centered at 0 before the PCA is computed. This is useful only if you have a strong bin/gene/etc. correlation and the resulting principal component has samples stacked vertically. This option is not applicable if the PCA is performed on the transposed matrix." truevalue="--rowCenter" falsevalue="" /> 53 <param argument="--rowCenter" type="boolean" label="Center Rows?" help="When specified, each row (bin, gene, etc.) in the matrix is centered at 0 before the PCA is computed. This is useful only if you have a strong bin/gene/etc. correlation and the resulting principal component has samples stacked vertically. This option is not applicable if the PCA is performed on the transposed matrix." truevalue="--rowCenter" falsevalue="" />
51 <param argument="--colors" type="text" name="colors" label="Symbol colors" value="" optional="True" 54 <param argument="--colors" type="text" name="colors" label="Symbol colors" value="" optional="True"
52 help="A list of colors for the symbols. Color names and html hex string (e.g., #eeff22) are accepted. The color names should be space separated. For example, --colors 'red blue green'. If not specified, the symbols will be given automatic colors." /> 55 help="A list of colors for the symbols. Color names and html hex string (e.g., #eeff22) are accepted. The color names should be space separated. For example, --colors 'red blue green'. If not specified, the symbols will be given automatic colors." />
56 <param argument="--markers" type="text" name="markers" label="Custom markers" value="" optional="True"
57 help="A list of markers for the symbols. (e.g., '&lt;','&gt;','o') are accepted. The marker values should be space separated. For example, 's' 'o' 's' 'o'. If not specified, the symbols will be given automatic shapes." />
53 </when> 58 </when>
54 </conditional> 59 </conditional>
55 </inputs> 60 </inputs>
56 <outputs> 61 <outputs>
57 <expand macro="output_image_file_format_not_nested" /> 62 <expand macro="output_image_file_format_not_nested" />